decalc.h

   1 #ifndef DECALC_H
   2 #define DECALC_H
   3 /*
   4  *  decalc.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 7/22/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "mothur.h"
  13 #include "sequence.hpp"
  14
  15 /***********************************************************************/
  16
  17 //This class was created using the algorythms described in the
  18 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper
  19 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
  20
  21 /***********************************************************************/
  22
  23 class DeCalculator {
  24
  25         public:
  26
  27                 DeCalculator() {};
  28                 ~DeCalculator() {};
  29
  30                 set<int> getPos() {  return h;  }
  31                 void setMask(string);
  32                 void setAlignmentLength(int l) {  alignLength = l;  }
  33                 void runMask(Sequence*);
  34                 void trimSeqs(Sequence*, Sequence*, map<int, int>&);
  35                 void removeObviousOutliers(vector< vector<float> >&);
  36                 vector<float> calcFreq(vector<Sequence*>, string);
  37                 vector<int> findWindows(Sequence*, int, int, int&, int);
  38                 vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
  39                 vector<float>  calcExpected(vector<float>, float);
  40                 vector<float>  findQav(vector<int>, int, vector<float>);
  41                 float calcDE(vector<float>, vector<float>);
  42                 float calcDist(Sequence*, Sequence*, int, int);
  43                 float getCoef(vector<float>, vector<float>);
  44                 vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
  45
  46         private:
  47                 float findAverage(vector<float> myVector);
  48                 string seqMask;
  49                 set<int> h;
  50                 int alignLength;
  51
  52 };
  53
  54 /***********************************************************************/
  55
  56 #endif